Genomic surveillance of antimicrobial resistance shows cattle are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico

Abstract

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a major public health concern globally. This study reports antibiotic susceptibility testing and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n=48) and ground beef (n=29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n=1637). The probability of finding MDR isolates was higher in ground beef as compared to lymph nodes: {chi}2=12.0, P=0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while over 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Occurrence of MDR isolates was strongly associated with NTS serovar ({chi}2=24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. Moreover, 100% of MDR isolates had mutations in the ramR gene. Among public NTS isolates from foods and clinical cases in Mexico to date, those from cattle had the highest proportion of MDR genotypes. Our results suggest attaining significant improvements in AMR meat safety may require the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.